{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T11:30:08Z","timestamp":1765279808948},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue\/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells\/organs in xenotransplantation and might eventually provide new targets in the \u03b11,3-galactosyltransferase gene-knock out pigs era.<\/jats:p>\n               <jats:p>Availability: The database can be accessed on the web at http:\/\/bioinformatics.snu.ac.kr\/xdb.<\/jats:p>\n               <jats:p>Contact: \u00a0byungkim@snu.ac.kr or ygkim@ssu.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt504","type":"journal-article","created":{"date-parts":[[2013,9,7]],"date-time":"2013-09-07T04:32:19Z","timestamp":1378528339000},"page":"2950-2952","source":"Crossref","is-referenced-by-count":4,"title":["The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire"],"prefix":"10.1093","volume":"29","author":[{"given":"Hae-Min","family":"Park","sequence":"first","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Ju-Hyeong","family":"Park","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Yoon-Woo","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Kyoung-Jin","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Hee-Jin","family":"Jeong","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Kyoung-Soon","family":"Jang","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Byung-Gee","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"},{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"},{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]},{"given":"Yun-Gon","family":"Kim","sequence":"additional","affiliation":[{"name":"1 School of Chemical and Biological Engineering and 2Department of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea 3Department of Chemical Engineering, Soongsil University, Seoul 156-743, Korea 4Institute of Molecular Biology and Genetics and 5Institute of Bioengineering, Seoul National University, Seoul 151-742, Korea"}]}],"member":"286","published-online":{"date-parts":[[2013,9,6]]},"reference":[{"key":"2023012810492116100_btt504-B1","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1093\/bioinformatics\/btn090","article-title":"GlycoBase and autoGU: tools for HPLC-based glycan analysis","volume":"24","author":"Campbell","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012810492116100_btt504-B2","doi-asserted-by":"crossref","first-page":"4117","DOI":"10.1002\/pmic.201100302","article-title":"UniCarbKB: putting the pieces together for glycomics research","volume":"11","author":"Campbell","year":"2011","journal-title":"Proteomics"},{"key":"2023012810492116100_btt504-B3","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gkg099","article-title":"GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update","volume":"31","author":"Cooper","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012810492116100_btt504-B4","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1111\/j.1440-1711.2005.01344.x","article-title":"Carbohydrates in xenotransplantation","volume":"83","author":"Ezzelarab","year":"2005","journal-title":"Immunol. Cell Biol."},{"key":"2023012810492116100_btt504-B5","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1002\/pmic.200900096","article-title":"Proposal for a standard system for drawing structural diagrams of N- and O-linked carbohydrates and related compounds","volume":"9","author":"Harvey","year":"2009","journal-title":"Proteomics"},{"key":"2023012810492116100_btt504-B6","doi-asserted-by":"crossref","first-page":"4719","DOI":"10.1021\/ac048350h","article-title":"A strategy for identification of oligosaccharide structures using observational multistage mass spectral library","volume":"77","author":"Kameyama","year":"2005","journal-title":"Anal. Chem."},{"key":"2023012810492116100_btt504-B7","doi-asserted-by":"crossref","first-page":"267","DOI":"10.4052\/tigg.18.267","article-title":"GlycoEpitope: the integrated database of carbohydrate antigens and antibodies","volume":"18","author":"Kawasaki","year":"2006","journal-title":"Trends Glycosci. Glyc."},{"key":"2023012810492116100_btt504-B8","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1002\/pmic.200500275","article-title":"The identification and characterization of xenoantigenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney","volume":"6","author":"Kim","year":"2006","journal-title":"Proteomics"},{"key":"2023012810492116100_btt504-B9","doi-asserted-by":"crossref","first-page":"2596","DOI":"10.1002\/pmic.200700972","article-title":"Structural analysis of alpha-Gal and new non-Gal carbohydrate epitopes from specific pathogen-free miniature pig kidney","volume":"8","author":"Kim","year":"2008","journal-title":"Proteomics"},{"key":"2023012810492116100_btt504-B10","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1002\/jms.1587","article-title":"Qualitative and quantitative comparison of N-glycans between pig endothelial and islet cells by high-performance liquid chromatography and mass spectrometry-based strategy","volume":"44","author":"Kim","year":"2009","journal-title":"J. Mass Spectrom."},{"key":"2023012810492116100_btt504-B11","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1002\/jms.1638","article-title":"Mass spectrometric analysis of the glycosphingolipid-derived glycans from miniature pig endothelial cells and islets: identification of NeuGc epitope in pig islets","volume":"44","author":"Kim","year":"2009","journal-title":"J. Mass Spectrom."},{"key":"2023012810492116100_btt504-B12","doi-asserted-by":"crossref","first-page":"877","DOI":"10.3109\/02713680903184243","article-title":"Identification of alpha-Gal and non-Gal epitopes in pig corneal endothelial cells and keratocytes by using mass spectrometry","volume":"34","author":"Kim","year":"2009","journal-title":"Curr. Eye Res."},{"key":"2023012810492116100_btt504-B13","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/j.cell.2006.08.019","article-title":"Glycosylation in cellular mechanisms of health and disease","volume":"126","author":"Ohtsubo","year":"2006","journal-title":"Cell"},{"key":"2023012810492116100_btt504-B14","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1097\/00007890-199312000-00031","article-title":"Carbohydrate antigens of pig tissues reacting with human natural antibodies as potential targets for hyperacute vascular rejection in pig-to-man organ xenotransplantation","volume":"56","author":"Oriol","year":"1993","journal-title":"Transplantation"},{"key":"2023012810492116100_btt504-B15","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.carres.2012.12.024","article-title":"Structural characterization of alpha-galactosylated O-glycans from miniature pig kidney and endothelial cells","volume":"369","author":"Park","year":"2013","journal-title":"Carbohydr. Res."},{"key":"2023012810492116100_btt504-B16","doi-asserted-by":"crossref","first-page":"82R","DOI":"10.1093\/glycob\/cwj080","article-title":"Advancing glycomics: implementation strategies at the consortium for functional glycomics","volume":"16","author":"Raman","year":"2006","journal-title":"Glycobiology"},{"key":"2023012810492116100_btt504-B17","doi-asserted-by":"crossref","first-page":"2370","DOI":"10.1126\/science.291.5512.2370","article-title":"Glycosylation and the immune system","volume":"291","author":"Rudd","year":"2001","journal-title":"Science"},{"key":"2023012810492116100_btt504-B18","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1128\/iai.13.2.600-607.1976","article-title":"Variability of the immunological state of germfree colostrum-deprived Minnesota miniature piglets","volume":"13","author":"Setcavage","year":"1976","journal-title":"Infect. Immun."},{"key":"2023012810492116100_btt504-B19","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/glycob\/cwq188","article-title":"EUROCarbDB: an open-access platform for glycoinformatics","volume":"21","author":"von der Lieth","year":"2011","journal-title":"Glycobiology"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/22\/2950\/48898610\/bioinformatics_29_22_2950.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/22\/2950\/48898610\/bioinformatics_29_22_2950.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:50:53Z","timestamp":1674910253000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/22\/2950\/315918"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,6]]},"references-count":19,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2013,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt504","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,11,15]]},"published":{"date-parts":[[2013,9,6]]}}}